The 33-year-old Brazilian centre-back was at home with 10 members of his family on Tuesday evening when a six-strong gang of armed men broke in shortly before midnight.
The masked intruders restrained those inside the property and escaped with cash and valuables including cameras, computers and jewels.
Hilton was slightly injured in the incident after being struck with a gun butt but did not require hospital treatment.
"Olympique Marseille can no longer tolerate and accept that some of their players should be victims of 'home-jacking'," read a club statement released on Wednesday.
"The club, which guarantees their safety in the context of their profession, now seeks to extend that protection to their private lives."
Marseille added that security patrols outside their players' properties would start "from tonight (Wednesday)".
Hilton is the latest in a growing list of Marseille players to have been targeted by armed robbers.
Argentine playmaker Lucho Gonzalez, one of the highest-paid footballers in France, was reportedly left traumatised after an armed gang attacked him and his family at his home in Aix-en-Provence in March.
"These are terrible things that can happen and which, from a psychological perspective, are traumatising," said OM coach Didier Deschamps at the time.
The home shared by Ghanaian brothers Andre and Jordan Ayew has been burgled twice, in November 2010 and May this year.
Other Marseille players, past and present, to have been victims of burglary include Stephane Mbia, Andre-Pierre Gignac, Mamadou Niang, Habib Beye and Fabien Barthez, as well as former president Jean-Claude Dassier.
Marseille sporting director Jose Anigo said that the spate of burglaries was putting off potential new signings.
"Every time I signed a player this year, the first questions they asked were: 'Can you guarantee security?', 'Are my family at risk?'" Anigo said during a press conference.
"Bringing players to OM in those conditions is complicated. You have to be a magician."